Validation

import numpy as np
import pandas as pd
import geopandas as gpd
import rasterio
from rasterio import features

import matplotlib.pyplot as plt
import sklearn
from sklearn.metrics import confusion_matrix, f1_score, accuracy_score, classification_report

from pathlib import Path
from IPython.display import display

import plotly.express as px
import plotly.figure_factory as ff
import plotly.graph_objects as go
import plotly.offline
plotly.offline.init_notebook_mode()

print('All libraries successfully imported!')
print(f'Scikit-learn: {sklearn.__version__}')

All libraries successfully imported!
Scikit-learn: 0.24.2

Set directory

computer_path = '/export/miro/ndeffense/LBRAT2104/'
grp_letter    = 'X'

lut_path  = f'{computer_path}data/LUT/'

# Directory for all work files
work_path = f'{computer_path}GROUP_{grp_letter}/WORK/'

in_situ_path = f'{work_path}IN_SITU/'
classif_path = f'{work_path}CLASSIF/'

am_path = f'{work_path}ACCURACY_METRICS/'


Path(am_path).mkdir(parents=True, exist_ok=True)

print(f'Accuracy Metrics path is set to : {am_path}')

Accuracy Metrics path is set to : /export/miro/ndeffense/LBRAT2104/GROUP_X/WORK/ACCURACY_METRICS/

Set parameters

site = 'NAMUR'
year = '2020'

no_data = 0

field_classif_code = 'sub_nb'
field_classif_name = 'sub'

Set filenames

s4s_lut_xlsx   = f'{lut_path}crop_dictionary_new.xlsx'

in_situ_val_shp = f'{in_situ_path}{site}_{year}_IN_SITU_ROI_VAL.shp'
in_situ_val_tif = f'{in_situ_path}{site}_{year}_IN_SITU_ROI_VAL.tif'

classif_tif = f'{classif_path}{site}_{year}_CLASSIF_RF_with_NDVI.tif'

cm_csv = f'{am_path}{site}_{year}_CM.csv'
cm_html = f'/export/miro/ndeffense/LBRAT2104/GIT/eo-toolbox/notebooks/7_Classification/figures/{site}_{year}_CM.html'
am_html = f'/export/miro/ndeffense/LBRAT2104/GIT/eo-toolbox/notebooks/7_Classification/figures/{site}_{year}_AM.html'

1. Prepare data

1.1 Rasterize in situ data validation shapefile

print(f'Raster template file : {classif_tif}')

# Open the shapefile with GeoPandas

in_situ_gdf = gpd.read_file(in_situ_val_shp)

# Open the raster file you want to use as a template for rasterize

src = rasterio.open(classif_tif, "r")

# Update metadata

out_meta = src.meta
out_meta.update(nodata=no_data)

crs_shp = str(in_situ_gdf.crs).split(":",1)[1]
crs_tif = str(src.crs).split(":",1)[1]

print(f'The CRS of in situ data is    : {crs_shp}')
print(f'The CRS of raster template is : {crs_tif}')

if crs_shp == crs_tif:
    print("CRS are the same")

    print(f'Rasterize starts : {in_situ_val_shp}')

    # Burn the features into the raster and write it out

    dst = rasterio.open(in_situ_val_tif, 'w+', **out_meta)
    dst_arr = dst.read(1)

    # This is where we create a generator of geom, value pairs to use in rasterizing

    geom_col = in_situ_gdf.geometry
    code_col = in_situ_gdf[field_classif_code].astype(int)

    shapes = ((geom,value) for geom, value in zip(geom_col, code_col))

    in_situ_arr = features.rasterize(shapes=shapes,
                                     fill=no_data,
                                     out=dst_arr,
                                     transform=dst.transform)
    
    dst.write_band(1, in_situ_arr)

    print(f'Rasterize is done : {in_situ_val_tif}')

    # Close rasterio objects
    src.close()
    dst.close()

else:
    print('CRS are different --> repoject in-situ data shapefile with "to_crs"')

Raster template file : /export/miro/ndeffense/LBRAT2104/GROUP_X/WORK/CLASSIF/NAMUR_2020_CLASSIF_RF_with_NDVI.tif
The CRS of in situ data is    : 32631
The CRS of raster template is : 32631
CRS are the same
Rasterize starts : /export/miro/ndeffense/LBRAT2104/GROUP_X/WORK/IN_SITU/NAMUR_2020_IN_SITU_ROI_VAL.shp
Rasterize is done : /export/miro/ndeffense/LBRAT2104/GROUP_X/WORK/IN_SITU/NAMUR_2020_IN_SITU_ROI_VAL_1.tif

1.2 Build y_pred and y_true

# Open in-situ used for validation
src = rasterio.open(in_situ_val_tif, "r")
val_arr = src.read(1)
src.close()

# Open classification map
src = rasterio.open(classif_tif, "r")
classif_arr = src.read(1)
src.close()

# Get the postion of validation pixels
idx = np.where(val_arr == no_data, 0, 1).astype(bool)

# Ground truth (correct) target values
y_true = val_arr[idx]

# Estimated targets as returned by a classifier.
y_pred = classif_arr[idx]

Sometimes, some classes do not appear in the classification map, they are not predicted by the Random Forest.

This means that some classes in y_true don't appear in y_pred.

classes_all  = sorted(np.unique(y_true))
classes_pred = sorted(np.unique(y_pred))

classes_missing = set(y_true) - set(y_pred)

print(f'{len(classes_missing)} classes are missing in the classification (y_pred) : {classes_missing} \n')

print(f'All training classes :\n {classes_all}')
print(f'All predicted classes (at least once) :\n {classes_pred}')

0 classes are missing in the classification (y_pred) : set() 

All training classes :
 [1111, 1121, 1152, 1171, 1192, 1435, 1511, 1771, 1811, 1911, 1923, 3199, 4111, 6999, 8111, 8411]
All predicted classes (at least once) :
 [1111, 1121, 1152, 1171, 1192, 1435, 1511, 1771, 1811, 1911, 1923, 3199, 4111, 6999, 8111, 8411]

1.3 Find class names

lut_df = pd.read_excel(s4s_lut_xlsx)

classes_name = lut_df[lut_df[field_classif_code].isin(classes_all)].sort_values(field_classif_code)[field_classif_name].to_list()

for code,name in zip(classes_all, classes_name):
    print(f'{code} - {name}')

1111 - Winter wheat
1121 - Maize
1152 - Barley six-row
1171 - Oats
1192 - Other cereals
1435 - Rapeseed
1511 - Potatoes
1771 - Peas
1811 - Sugar beet
1911 - Alfalfa
1923 - Flax, hemp and other similar crops
3199 - Grassland and meadows
4111 - Fallows 1 year
6999 - Forest
8111 - Urban
8411 - Greenhouses

2. Confusion Matrix

2.1 Compute Confusion Matrix

cm = confusion_matrix(y_true, y_pred)

cm_df = pd.DataFrame(cm)

cm_values = cm_df.values

cm_df.columns = classes_all
cm_df.index = classes_all

cm_df.to_csv(cm_csv, index=True, sep=',')

display(cm_df)

	1111	1121	1152	1171	1192	1435	1511	1771	1811	1911	1923	3199	4111	6999	8111	8411
1111	18463	5	2077	130	1237	58	0	0	0	0	114	65	4	1	64	9
1121	0	5026	0	1	0	12	266	0	1061	0	0	112	0	0	28	0
1152	214	0	4307	241	7	14	0	0	0	0	0	239	0	0	1	0
1171	75	3	0	203	0	0	0	0	0	0	4	0	1	0	0	0
1192	3307	64	8	132	667	0	0	9	0	0	165	222	0	0	4	13
1435	23	0	7	0	0	423	0	0	0	0	0	38	0	0	7	0
1511	0	1969	0	0	0	0	2859	0	0	0	0	1	0	1	8	0
1771	7	0	0	0	0	0	2	892	0	0	2	0	0	0	125	0
1811	2	153	0	0	0	0	238	0	5190	0	0	9	4	0	0	0
1911	0	0	0	0	0	0	0	0	0	0	0	151	0	0	0	0
1923	12	0	0	14	0	0	0	0	0	0	897	1	0	0	7	0
3199	5	0	13	4	0	4	0	1	0	18	0	17384	3	340	152	1
4111	0	0	0	0	0	0	3	0	0	0	0	44	2	0	0	0
6999	6	0	0	0	0	0	0	0	0	0	0	32	0	702	38	0
8111	8	0	0	0	0	0	0	0	0	0	0	2	0	0	502	0
8411	0	30	0	0	0	0	0	66	6	0	0	0	0	0	57	0

2.2 Plot Confusion Matrix

# invert z idx values
z = cm[::-1]

x = classes_name
y = x[::-1].copy() # invert idx values of x

# change each element of z to type string for annotations
z_text = [[str(y) for y in x] for x in z]

# set up figure 
fig = ff.create_annotated_heatmap(z,
                                  x=x,
                                  y=y,
                                  annotation_text=z_text,
                                  colorscale='spectral',
                                  reversescale=True)

# add title
fig.update_layout(title_text=f"Confusion Matrix - {site}, {year}")

# adjust margins to make room for yaxis title
#fig.update_layout(margin=dict(t=200, l=200))

#fig.update_xaxes(tickfont_size=20)
#fig.update_yaxes(tickfont_size=20)
#fig.update_layout(font_size=25)

# add colorbar
#fig['data'][0]['showscale'] = True

fig.show()
fig.write_html(cm_html, full_html=False)

3. Accuracy metrics

3.1 Compute Accuracy Metrics

If you decide that you are not interested in the scores of classes that were not predicted, then you can explicitly specify the classes you are interested in (which are labels that were predicted at least once).

acc_metrics_str  = classification_report(y_true,
                                         y_pred,
                                         target_names=classes_name,
                                         labels=classes_all,
                                         digits=3)

print(acc_metrics_str)

                                    precision    recall  f1-score   support

                      Winter wheat      0.835     0.831     0.833     22227
                             Maize      0.693     0.773     0.731      6506
                    Barley six-row      0.672     0.857     0.753      5023
                              Oats      0.280     0.710     0.402       286
                     Other cereals      0.349     0.145     0.205      4591
                          Rapeseed      0.828     0.849     0.838       498
                          Potatoes      0.849     0.591     0.697      4838
                              Peas      0.921     0.868     0.894      1028
                        Sugar beet      0.829     0.927     0.876      5596
                           Alfalfa      0.000     0.000     0.000       151
Flax, hemp and other similar crops      0.759     0.963     0.849       931
             Grassland and meadows      0.950     0.970     0.960     17925
                    Fallows 1 year      0.143     0.041     0.063        49
                            Forest      0.672     0.902     0.771       778
                             Urban      0.506     0.980     0.667       512
                       Greenhouses      0.000     0.000     0.000       159

                          accuracy                          0.809     71098
                         macro avg      0.580     0.651     0.596     71098
                      weighted avg      0.798     0.809     0.797     71098

3.2 Compute Overall Accuracy

oa = accuracy_score(y_true, y_pred)
oa = round(oa*100, 2)

print(f'Overall Accuracy : {oa}%')

Overall Accuracy : 80.9%

3.3 Plot Accuracy Metrics

acc_metrics_dict = classification_report(y_true, y_pred,target_names=classes_name, output_dict=True)

am_df = pd.DataFrame.from_dict(acc_metrics_dict).round(3)

am_df = am_df.iloc[:,:-3]

#am_df = pd.concat([am_df, nb_df])

#am_df = am_df.sort_values(by='pix_count', ascending=False, axis=1)

class_name = am_df.columns.to_list()
precision = am_df.loc['precision'].to_list()
recall    = am_df.loc['recall'].to_list()
f1_score  = am_df.loc['f1-score'].to_list()

fig = go.Figure(data=[
    go.Bar(name='Precision', x=class_name, y=precision, text=precision, textposition='auto'),
    go.Bar(name='Recall', x=class_name, y=recall, text=recall, textposition='auto'),
    go.Bar(name='F1-score', x=class_name, y=f1_score, text=f1_score, textposition='auto')
])
# Change the bar mode
fig.update_layout(title_text=f'Accuracy Metrics - {site}, {year}',
                  barmode='group')

#fig.update_xaxes(tickfont_size=30)
fig.update_yaxes(tickfont_size=10, range=[0,1])
#fig.update_layout(xaxis_title=None, font_size=10)
#fig.update_layout(legend=dict(font=dict(size=25)))

fig.show()
fig.write_html(am_html, full_html=False)